5NGE

Crystal structure of USP7 in complex with the non-covalent inhibitor, FT671


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Molecular basis of USP7 inhibition by selective small-molecule inhibitors.

Turnbull, A.P.Ioannidis, S.Krajewski, W.W.Pinto-Fernandez, A.Heride, C.Martin, A.C.L.Tonkin, L.M.Townsend, E.C.Buker, S.M.Lancia, D.R.Caravella, J.A.Toms, A.V.Charlton, T.M.Lahdenranta, J.Wilker, E.Follows, B.C.Evans, N.J.Stead, L.Alli, C.Zarayskiy, V.V.Talbot, A.C.Buckmelter, A.J.Wang, M.McKinnon, C.L.Saab, F.McGouran, J.F.Century, H.Gersch, M.Pittman, M.S.Marshall, C.G.Raynham, T.M.Simcox, M.Stewart, L.M.D.McLoughlin, S.B.Escobedo, J.A.Bair, K.W.Dinsmore, C.J.Hammonds, T.R.Kim, S.Urbe, S.Clague, M.J.Kessler, B.M.Komander, D.

(2017) Nature 550: 481-486

  • DOI: https://doi.org/10.1038/nature24451
  • Primary Citation of Related Structures:  
    5NGE, 5NGF

  • PubMed Abstract: 

    Ubiquitination controls the stability of most cellular proteins, and its deregulation contributes to human diseases including cancer. Deubiquitinases remove ubiquitin from proteins, and their inhibition can induce the degradation of selected proteins, potentially including otherwise 'undruggable' targets. For example, the inhibition of ubiquitin-specific protease 7 (USP7) results in the degradation of the oncogenic E3 ligase MDM2, and leads to re-activation of the tumour suppressor p53 in various cancers. Here we report that two compounds, FT671 and FT827, inhibit USP7 with high affinity and specificity in vitro and within human cells. Co-crystal structures reveal that both compounds target a dynamic pocket near the catalytic centre of the auto-inhibited apo form of USP7, which differs from other USP deubiquitinases. Consistent with USP7 target engagement in cells, FT671 destabilizes USP7 substrates including MDM2, increases levels of p53, and results in the transcription of p53 target genes, induction of the tumour suppressor p21, and inhibition of tumour growth in mice.


  • Organizational Affiliation

    CRUK Therapeutic Discovery Laboratories, London Bioscience Innovation Centre, London NW1 0NH, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 7
A, B
355Homo sapiensMutation(s): 0 
Gene Names: USP7HAUSP
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q93009 (Homo sapiens)
Explore Q93009 
Go to UniProtKB:  Q93009
PHAROS:  Q93009
GTEx:  ENSG00000187555 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93009
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8WK
Query on 8WK

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
5-[[1-[(3~{S})-4,4-bis(fluoranyl)-3-(3-fluoranylpyrazol-1-yl)butanoyl]-4-oxidanyl-piperidin-4-yl]methyl]-1-(4-fluorophenyl)pyrazolo[3,4-d]pyrimidin-4-one
C24 H23 F4 N7 O3
BLSNYSFLZAWBIV-SFHVURJKSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.28α = 90
b = 70.3β = 97.17
c = 78.56γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2017-10-25
    Changes: Structure summary
  • Version 1.2: 2017-11-01
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Database references
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Refinement description